[Bioperl-l] Bioperl 1.5.2 RC2

Chris Fields cjfields at uiuc.edu
Tue Oct 17 20:51:35 EDT 2006


On Oct 17, 2006, at 6:49 PM, Paul Boutros wrote:

> Hi Chris,
>
> Yup, that's it.  I installed XML::SAX::ExpatXS (make test output
> below).  Should there be a note somewhere in the INSTALL docs saying
> basically what you just wrote?  Or maybe it's already there somewhere
> and I missed it.

The INSTALL docs should have this, yes.  I'll double-check though.

Pretty much anything that plugs into XML::SAX except XML::SAX::Expat  
works (XML::LibXML also works, I found).

> Also, I'd propose changing BioDBSeqFeature_mysql.t so that it checks
> if DBD::mysql can be loaded, and if not doesn't run the test.  Since
> the file is only one-line long, here's the modified file rather than a
> patch:
> ################################################################
> BEGIN {
>          # DBD::mysql is required
>          eval {
>                  require DBD::mysql;
>                  };
>          if ( $@ ) {
>                  use Test::More skip_all => "DBD::mysql is not
> installed or is installed incorrectly - skipping BioDBSeqFeature
> _mysql.t";
>                  exit(0);
>                  }
>          }
>
> system "perl t/BioDBSeqFeature.t -adaptor DBI::mysql -create 1 -temp 1
> -dsn test";
> ################################################################
>
> And when I run it I get:
> t/BioDBSeqFeature_mysql......skipped
>          all skipped: DBD::mysql is not installed or is installed
> incorrectly - skipping BioDBSeqFeature_mysql.t
>
> And for the overall make test:
> All tests successful, 3 tests and 106 subtests skipped.
> Files=236, Tests=11642, 247 wallclock secs (143.85 cusr + 20.39 csys =
> 164.24 CPU)

It should check this when using 'perl Makefile.PL', since the tests  
are only set up if MySQL is present (so you would assume that it  
checks for DBD::mysql).  I'll look into it.

Chris

> Hope this helps,
> Paul
>
>
> Quoting Chris Fields <cjfields at uiuc.edu>:
>
>> Your local copy of XML::SAX has XML::SAX::Expat set as the default  
>> SAX
>> backend parser.  For some reason BLAST XML parsing doesn't work  
>> with that
>> parser (it tries to verify the XML first before parsing, hence the  
>> DTD
>> error).  I may try getting this to work again, but so far I  
>> haven't found an
>> easy way to prevent XML verification via XML::SAX::Expat.
>>
>> There are two options: 1) install XML::SAX::ExpatXS (the better  
>> option),
>> which works AND is 4x faster than XML::SAX::Expat, or  2) set the  
>> default
>> parser in the PareserDetails.ini file in your local to use
>> XML::SAX::PurePerl.
>>
>> BTW, XML::SAX::ExpatXS is intended to replace XML::SAX::Expat (it  
>> just
>> hasn't officially happened yet); the latter hasn't had significant
>> development in about three years.
>>
>> Christopher Fields
>> Postdoctoral Researcher - Switzer Lab
>> Dept. of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>> -----Original Message-----
>>> From: Paul Boutros [mailto:paul.boutros at utoronto.ca]
>>> Sent: Tuesday, October 17, 2006 1:00 PM
>>> To: Chris Fields
>>> Cc: bioperl-l at lists.open-bio.org
>>> Subject: RE: [Bioperl-l] Bioperl 1.5.2 RC2
>>>
>>> Hi Chris,
>>>
>>> Here it is:
>>> pcboutro at ccb690[643] >> perl -I. t/SearchIO.t
>>> 1..1337
>>> ok 1
>>>
>>> -------------------- WARNING ---------------------
>>> MSG: XML::SAX::Expat not currently supported; must have local copies
>>> of NCBI DTD docs!
>>> ---------------------------------------------------
>>>
>>> -------------------- WARNING ---------------------
>>> MSG: error in parsing a report:
>>>
>>> 404 File `/home/pcboutro/tmp/bioperl-1.5.2-RC2/NCBI_BlastOutput.dtd'
>>> does not exist
>>> file:///home/pcboutro/tmp/bioperl-1.5.2-RC2/NCBI_BlastOutput.dtd
>>> Handler couldn't resolve external entity at line 2, column 82,  
>>> byte 104
>>> error in processing external entity reference at line 2, column 82,
>>> byte 104 at
>>> /db2blast/perl/lib/site_perl/5.8.8/aix-thread-multi/XML/Parser.pm  
>>> line
>>> 187
>>>
>>> ---------------------------------------------------
>>> not ok 2
>>> # Failed test 2 in t/SearchIO.t at line 68
>>> Can't call method "database_name" on an undefined value at
>>> t/SearchIO.t line 69.
>>>
>>>
>>> Quoting Chris Fields <cjfields at uiuc.edu>:
>>>
>>>> What do you get when you run the SearchIO.t test by itself using  
>>>> 'perl -
>>> I.
>>>> t/SearchIO.t'?  It looks like something pretty catastrophic  
>>>> happened.
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher - Switzer Lab
>>>> Dept. of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>> bounces at lists.open-bio.org] On Behalf Of Paul Boutros
>>>>> Sent: Tuesday, October 17, 2006 11:57 AM
>>>>> To: bioperl-l at lists.open-bio.org
>>>>> Subject: Re: [Bioperl-l] Bioperl 1.5.2 RC2
>>>>>
>>>>> Hi,
>>>>> Here's a quick make test on AIX 5.2 with Perl 5.8.8.  I get two  
>>>>> failed
>>>>> tests, the first seems to be just a result of me not having  
>>>>> DBD::mysql
>>>>> installed.
>>>>> Paul
>>>>>
>>>>> Test Summary
>>>>> ============
>>>>>
>>>>> Failed Test               Stat Wstat Total Fail  List of Failed
>>>>> ------------------------------------------------------------------ 
>>>>> -----
>>> ---
>>>>> -----
>>>>> t/BioDBSeqFeature_mysql.t               46   46  1-46
>>>>> t/SearchIO.t                22  5632  1337 2671  2-1337
>>>>> 2 tests and 106 subtests skipped.
>>>>> Failed 2/236 test scripts. 1382/11688 subtests failed.
>>>>> Files=236, Tests=11688, 259 wallclock secs (139.47 cusr + 20.14  
>>>>> csys =
>>>>> 159.61 CPU)
>>>>>
>>>>> BioDBSeqFeature_mysql
>>>>> =====================
>>>>> pcboutro at ccb690[674] >> perl -w t/BioDBSeqFeature_mysql.t
>>>>> 1..46
>>>>> install_driver(mysql) failed: Can't locate DBD/mysql.pm in @INC  
>>>>> (@INC
>>>>> contains: /home/pcboutro/cvswork/bioperl-live/ . .. ./blib/lib t
>>>>> /db2blast/perl/lib/5.8.8/aix-thread-multi /db2blast/perl/lib/5.8.8
>>>>> /db2blast/perl/lib/site_perl/5.8.8/aix-thread-multi
>>>>> /db2blast/perl/lib/site_perl/5.8.8 /db2blast/perl/lib/ 
>>>>> site_perl) at
>>>>> (eval 37) line 3.
>>>>> Perhaps the DBD::mysql perl module hasn't been fully installed,
>>>>> or perhaps the capitalisation of 'mysql' isn't right.
>>>>> Available drivers: DB2, DBM, ExampleP, File, Proxy, Sponge.
>>>>>   at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 208
>>>>>
>>>>> SearchIO
>>>>> ========
>>>>> pcboutro at ccb690[670] >> perl -w t/SearchIO.t | more
>>>>> 1..1337
>>>>> ok 1
>>>>>
>>>>> -------------------- WARNING ---------------------
>>>>> MSG: XML::SAX::Expat not currently supported; must have local  
>>>>> copies
>>>>> of NCBI DTD docs!
>>>>> ---------------------------------------------------
>>>>>
>>>>> -------------------- WARNING ---------------------
>>>>> MSG: error in parsing a report:
>>>>>
>>>>> 404 File `/home/pcboutro/tmp/bioperl-1.5.2-RC2/ 
>>>>> NCBI_BlastOutput.dtd'
>>>>> does not exist
>>>>> file:///home/pcboutro/tmp/bioperl-1.5.2-RC2/NCBI_BlastOutput.dtd
>>>>> Handler couldn't resolve external entity at line 2, column 82,  
>>>>> byte 104
>>>>> error in processing external entity reference at line 2, column  
>>>>> 82,
>>>>> byte 104 at
>>>>> /db2blast/perl/lib/site_perl/5.8.8/aix-thread-multi/XML/ 
>>>>> Parser.pm line
>>>>> 187
>>>>>
>>>>> ---------------------------------------------------
>>>>> not ok 2
>>>>> # Failed test 2 in t/SearchIO.t at line 68
>>>>> Can't call method "database_name" on an undefined value at
>>>>> t/SearchIO.t line 69.
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> Message: 10
>>>>> Date: Tue, 17 Oct 2006 11:32:54 +0100
>>>>> From: Sendu Bala <bix at sendu.me.uk>
>>>>> Subject: [Bioperl-l] Bioperl 1.5.2 RC2
>>>>> To: bioperl-l at bioperl.org
>>>>> Message-ID: <4534B156.4090501 at sendu.me.uk>
>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>>
>>>>> Bioperl 1.5.2 Release Candidate 2 is ready and available for  
>>>>> testing.
>>>>> See http://www.bioperl.org/wiki/Release_1.5.2 for
>>>>> instructions on getting and testing this RC.
>>>>>
>>>>> Developers:
>>>>>     This should be the last RC before release ~next monday. Now  
>>>>> would
>>>>>     be a good time for last minute documentaiton updates and  
>>>>> additions.
>>>>>
>>>>> Users:
>>>>>     Even though 1.5.2 is a 'developer' release, we consider it  
>>>>> the most
>>>>>     stable and capable version of Bioperl, and recommend that  
>>>>> you use
>>>>>     it in all but the most critical production environments.  
>>>>> Please
>>>>>     try it out and let us know of any problems or difficulties  
>>>>> you run
>>>>>     into.
>>>>>
>>>>>
>>>>> Thank you,
>>>>> Sendu.
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>
>>
>>
>>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





More information about the Bioperl-l mailing list